Database : The Journal of Biological Databases and Curation This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.

The Breeding Information Management System (BIMS): an online resource for crop breeding
AbstractIn this era of big data, breeding programs are producing ever larger amounts of data. This necessitates access to efficient management systems to keep track of cross, performance, pedigree, geographical and image-based data, as well as genotyping data. In this article, we report the progress on the Breeding Information Management System (BIMS), a free, secure and online breeding management system that allows breeders to store, manage, archive and analyze their private breeding data. BIMS is the first publicly available database system that enables individual breeders to integrate their private phenotypic and genoty...
Source: Database : The Journal of Biological Databases and Curation - August 20, 2021 Category: Databases & Libraries Source Type: research

Nabe: an energetic database of amino acid mutations in protein –nucleic acid binding interfaces
AbstractProtein –nucleic acid complexes play essential roles in regulating transcription, translation, DNA replication, repair and recombination, RNA processing and translocation. Site-directed mutagenesis has been extremely useful in understanding the principles of protein–DNA and protein–RNA interactions, a nd experimentally determined mutagenesis data are prerequisites for designing effective algorithms for predicting the binding affinity change upon mutation. However, a vital challenge in this area is the lack of sufficient public experimentally recognized mutation data, which leads to difficulties i n developing...
Source: Database : The Journal of Biological Databases and Curation - August 14, 2021 Category: Databases & Libraries Source Type: research

A PostgreSQL Tripal solution for large-scale genotypic and phenotypic data
We describe here a fully relational PostgreSQL solution to handle large-scale genotypic and phenotypic data that is implemented as a collection of freely available, open-source modules. These Tripal extension modules provide a holistic approach for importing, storage, display and analysis within a relational database schema. Furthermore, they embody the Tripal approach to FAIR data by providing multiple search tools and ensuring metadata is fully described and interoperable. Our solution focuses on data integrity, as well as optimizing performance to provide a fully functional system that is currently being used in the pro...
Source: Database : The Journal of Biological Databases and Curation - August 14, 2021 Category: Databases & Libraries Source Type: research

A nomenclature for echinoderm genes
AbstractEchinoderm embryos and larvae are prominent experimental model systems for studying developmental mechanisms. High-quality, assembled, annotated genome sequences are now available for several echinoderm species, including representatives from most classes. The increased availability of these data necessitates the development of a nomenclature that assigns universally interpretable gene symbols to echinoderm genes to facilitate cross-species comparisons of gene functions, both within echinoderms and across other phyla. This paper describes the implementation of an improved set of echinoderm gene nomenclature guideli...
Source: Database : The Journal of Biological Databases and Curation - August 13, 2021 Category: Databases & Libraries Source Type: research

Male Infertility Knowledgebase: decoding the genetic and disease landscape
AbstractMale infertility is a multifactorial condition that contributes to around one-third of cases of infertility worldwide. Several chromosomal aberrations, single-gene and polygenic associations with male factor defects have been reported. These defects manifest as sperm number or sperm quality defects leading to infertility. However, in almost 40% of cases, the genetic etiology of male infertility remains unexplained. Understanding the causal genetic factors is crucial for effective patient management and counseling. Integrating the vast amount of available omics data on male infertility is a first step towards unders...
Source: Database : The Journal of Biological Databases and Curation - August 7, 2021 Category: Databases & Libraries Source Type: research

Functionathon: a manual data mining workflow to generate functional hypotheses for uncharacterized human proteins and its application by undergraduate students
AbstractAbout 10% of human proteins have no annotated function in protein knowledge bases. A workflow to generate hypotheses for the function of these uncharacterized proteins has been developed, based on predicted and experimental information on protein properties, interactions, tissular expression, subcellular localization, conservation in other organisms, as well as phenotypic data in mutant model organisms. This workflow has been applied to seven uncharacterized human proteins (C6orf118, C7orf25, CXorf58, RSRP1, SMLR1, TMEM53 and TMEM232) in the frame of a course-based undergraduate research experience named Functionat...
Source: Database : The Journal of Biological Databases and Curation - July 28, 2021 Category: Databases & Libraries Source Type: research

MUSTARD —a comprehensive resource of mutation-specific therapies in cancer
AbstractThe steady increase in global cancer burden has fuelled the development of several modes of treatment for the disease. In the presence of an actionable mutation, targeted therapies offer a method to selectively attack cancer cells, increasing overall efficacy and reducing harmful side effects. However, different drug molecules are in different stages of development, with new molecules obtaining approvals from regulatory agencies each year. To augment clinical impact, it is important that this information reaches clinicians, patients and researchers swiftly and in a structured, well-annotated manner. To this end, we...
Source: Database : The Journal of Biological Databases and Curation - July 26, 2021 Category: Databases & Libraries Source Type: research

Web tools to perform long non-coding RNAs analysis in oncology research
AbstractAccumulated evidence suggests that the widely expressed long-non-coding RNAs (lncRNAs) are involved in biogenesis. Some aberrant lncRNAs are closely related to pathological changes, for instance, in cancer. Both in tumorigenesis and cancer progression, depending on the interplay with cellular molecules, lncRNAs can modulate transcriptional interference, chromatin remodeling, post-translational regulation and protein modification, and further interfere with signaling pathways. Aiming to the diagnosis/ prognosis markers or potential therapeutical targets, it is important to figure out the specific mechanism and the t...
Source: Database : The Journal of Biological Databases and Curation - July 23, 2021 Category: Databases & Libraries Source Type: research

circExp database: an online transcriptome platform for human circRNA expressions in cancers
AbstractCircular RNA (circRNA) is a highly stable, single-stranded, closed-loop RNA that works as RNA or as a protein decoy to regulate gene expression. In humans, thousands of circRNA transcriptional products precisely express in specific developmental stages, tissues and cell types. Due to their stability and specificity, circRNAs are ideal biomarkers for cancer diagnosis and prognosis. To provide an integrated and standardized circRNA expression profile for human cancers, we performed extensive data curation across 11 technical platforms, collecting 48 expression profile data sets for 18 cancer types and amassing 860 �...
Source: Database : The Journal of Biological Databases and Curation - July 23, 2021 Category: Databases & Libraries Source Type: research

Automatization and self-maintenance of the O-GlcNAcome catalog: a smart scientific database
AbstractPost-translational modifications (PTMs) are ubiquitous and essential for protein function and signaling, motivating the need for sustainable benefit and open models of web databases. Highly conservedO-GlcNAcylation is a case example of one of the most recently discovered PTMs, investigated by a growing community. Historically, details aboutO-GlcNAcylated proteins and sites were dispersed across literature and in non-O-GlcNAc-focused, rapidly outdated or now defunct web databases. In a first effort to fill the gap, we recently published a humanO-GlcNAcome catalog with a basic web interface. Based on the enthusiasm g...
Source: Database : The Journal of Biological Databases and Curation - July 19, 2021 Category: Databases & Libraries Source Type: research

The Progenetix oncogenomic resource in 2021
AbstractIn cancer, copy number aberrations (CNAs) represent a type of nearly ubiquitous and frequently extensive structural genome variations. To disentangle the molecular mechanisms underlying tumorigenesis as well as identify and characterize molecular subtypes, the comparative and meta-analysis of large genomic variant collections can be of immense importance. Over the last decades, cancer genomic profiling projects have resulted in a large amount of somatic genome variation profiles, however segregated in a multitude of individual studies and datasets. The Progenetix project, initiated in 2001, curates individual cance...
Source: Database : The Journal of Biological Databases and Curation - July 17, 2021 Category: Databases & Libraries Source Type: research

CNVIntegrate: the first multi-ethnic database for identifying copy number variations associated with cancer
AbstractHuman copy number variations (CNVs) and copy number alterations (CNAs) are DNA segments (>1000 base pairs) of duplications or deletions with respect to the reference genome, potentially causing genomic imbalance leading to diseases such as cancer. CNVs further cause genetic diversity in healthy populations and are predominant drivers of gene/genome evolution. Initiatives have been taken by the research community to establish large-scale databases to comprehensively characterize CNVs in humans. Exome Aggregation Consortium (ExAC) is one such endeavor that catalogs CNVs, of nearly 60 000 healthy individuals acr...
Source: Database : The Journal of Biological Databases and Curation - July 14, 2021 Category: Databases & Libraries Source Type: research

Standardization of assay representation in the Ontology for Biomedical Investigations
We describe here this informative and productive process to describe the specific benefits and obstacles for OBI and the universal lessons for similar projects. (Source: Database : The Journal of Biological Databases and Curation)
Source: Database : The Journal of Biological Databases and Curation - July 9, 2021 Category: Databases & Libraries Source Type: research

TIDB: a comprehensive database of trained immunity
AbstractTrained immunity is a newly emerging concept that defines the ability of the innate immune system to form immune memory and provide long-lasting protection against previously encountered antigens. Accumulating evidence reveals that trained immunity not only has broad benefits to host defense but is also harmful to the host in chronic inflammatory diseases. However, all trained immunity-related information is scattered in the literature and thus is difficult to access. Here, we describe Trained Immunity DataBase (TIDB), a comprehensive database that provides well-studied trained immunity-related genes from human, ra...
Source: Database : The Journal of Biological Databases and Curation - July 9, 2021 Category: Databases & Libraries Source Type: research

KMDATA: a curated database of reconstructed individual patient-level data from 153 oncology clinical trials
AbstractWe created a database of reconstructed patient-level data from published clinical trials that includes multiple time-to-event outcomes such as overall survival and progression-free survival. Outcomes were extracted from Kaplan –Meier (KM) curves reported in 153 oncology Phase III clinical trial publications identified through a PubMed search of clinical trials in breast, lung, prostate and colorectal cancer, published between 2014 and 2016. For each trial that met our search criteria, we curated study-level information and digitized all reported KM curves with the softwareDigitizelt. We then used the digitized KM...
Source: Database : The Journal of Biological Databases and Curation - June 26, 2021 Category: Databases & Libraries Source Type: research